def import_shares():
admin = User.objects.get(username='******')
select = """SELECT
sp.description,
sp.random_dir,
sp.submitted,
p.description as pdescription,
p.project_title as ptitle,
g.db_group,
t.type as type,
t.description as type_description
FROM sub_project sp join project p on sp.project_id = p.project_id join type t on sp.type_id = t.type_id join db_group g on g.group_id = p.group_id"""
subprojects = dictfetchall(select)
for sp in subprojects:
share_id = '00000%s'%sp['random_dir']
try:
share = Share.objects.get(id=share_id)
share.delete()
except:
pass
share = Share(id=share_id)
share.name = ('%s: %s- %s, %s'%(sp['db_group'],sp['ptitle'],sp['type'],sp['submitted']))[:99]
print 'Creating %s'%share.name[:99]
share.notes = "Project Description:%s\nSubproject Description:%s"%(sp['pdescription'],sp['description'])
share.owner=admin
share.created = sp['submitted']
share.save()
tag = Tag.objects.get_or_create(name=sp['db_group'])[0]
share.tags.add(tag)
share.save()
def import_permissions():
admin = User.objects.get(username='******')
select = """SELECT random_dir, login, permission FROM
(
SELECT sub_project_id, login, user.user_id, lastname, firstname, permission FROM all_user_group_permission, project, sub_project, user WHERE sub_project.project_id = project.project_id AND all_user_group_permission.group_id = project.group_id AND all_user_group_permission.user_id = user.user_id
UNION
SELECT sub_project_id, login, user.user_id, lastname, firstname, permission FROM all_user_sub_project_permission, user WHERE source LIKE 'project' AND all_user_sub_project_permission.user_id = user.user_id
UNION
SELECT sub_project_id, login, user.user_id, lastname, firstname, permission FROM all_user_sub_project_permission, user WHERE source LIKE 'sub_project' AND all_user_sub_project_permission.user_id = user.user_id
) as X join sub_project sp on X.sub_project_id = sp.sub_project_id
GROUP BY random_dir,login,permission
ORDER BY random_dir,lastname, user_id, permission"""
perms = dictfetchall(select)
perm_map = {
'administer': 'admin',
'view-project': 'view_share_files',
'view-files': 'download_share_files',
'upload-files': 'write_to_share',
'delete-files': 'delete_share_files'
}
for p in perms:
share_id = '00000%s' % p['random_dir']
print 'treating share %s' % share_id
share = Share.objects.get(id=share_id)
user = User.objects.get(email=p['login'])
assign_perm(perm_map[p['permission']], user, share)
def import_shares():
admin = User.objects.get(username='******')
select = """SELECT
sp.description,
sp.random_dir,
sp.submitted,
p.description as pdescription,
p.project_title as ptitle,
g.db_group,
t.type as type,
t.description as type_description
FROM sub_project sp join project p on sp.project_id = p.project_id join type t on sp.type_id = t.type_id join db_group g on g.group_id = p.group_id"""
subprojects = dictfetchall(select)
for sp in subprojects:
share_id = '00000%s' % sp['random_dir']
try:
share = Share.objects.get(id=share_id)
share.delete()
except:
pass
share = Share(id=share_id)
share.name = (
'%s: %s- %s, %s' %
(sp['db_group'], sp['ptitle'], sp['type'], sp['submitted']))[:99]
print 'Creating %s' % share.name[:99]
share.notes = "Project Description:%s\nSubproject Description:%s" % (
sp['pdescription'], sp['description'])
share.owner = admin
share.created = sp['submitted']
share.save()
tag = Tag.objects.get_or_create(name=sp['db_group'])[0]
share.tags.add(tag)
share.save()
def get_table_rows(conn, table, limit=None, offset=None, order=None):
try:
with conn.cursor() as c:
c.execute(query_gen.get_table_rows_query(table, limit, offset))
return db.dictfetchall(c)
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def get_table_query_row_count(conn, table, filters, limit=None, offset=None, order=None):
try:
with conn.cursor() as c:
query, params = query_gen.get_filtered_rows_query(table, filters, limit, offset, order)
c.execute(query_gen.get_row_count_query(query), params)
return db.dictfetchall(c)[0]
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def get_function_rows(conn, function, args, limit=None, offset=None, order=None):
try:
with conn.cursor() as c:
query, _args = query_gen.get_function_query(function, args, limit, offset, order)
c.execute(query, _args)
return db.dictfetchall(c)
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def insert_table_row(conn, table, obj):
try:
params = [obj[x] for x in obj]
with conn.cursor() as c:
c.execute(query_gen.insert_table_row_query(table, obj), params)
rows = db.dictfetchall(c)
if len(rows) > 0:
return rows
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def insert_table_rows(conn, table, objs):
try:
copy_stmt, insert_buffer = query_gen.insert_table_rows_query(table, objs)
with conn.cursor() as c:
c.copy_expert(copy_stmt, insert_buffer)
rows = db.dictfetchall(c)
if len(rows) > 0:
return rows
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def get_table_row(conn, table, pk):
try:
with conn.cursor() as c:
c.execute(query_gen.get_table_row_query(schema.PKS, table, pk), [pk])
rows = db.dictfetchall(c)
if len(rows) > 0:
return rows
return None
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def update_creation_date():
select = "SELECT random_dir, submitted FROM sub_project"
subprojects = dictfetchall(select)
for sp in subprojects:
share_id = '00000%s' % sp['random_dir']
try:
share = Share.objects.get(id=share_id)
share.created = sp['submitted']
share.save()
except:
pass
def update_table_row(conn, table, pk, obj):
try:
query = query_gen.update_table_row_query(schema.PKS, table, obj)
params = [obj[x] for x in obj] + [pk]
with conn.cursor() as c:
c.execute(query, params)
rows = db.dictfetchall(c)
if len(rows) > 0:
return rows
except (query_gen.QueryGenError, psycopg2.DataError, psycopg2.IntegrityError), e:
raise_bad_request(str(e))
def update_creation_date():
select = "SELECT random_dir, submitted FROM sub_project"
subprojects = dictfetchall(select)
for sp in subprojects:
share_id = '00000%s'%sp['random_dir']
try:
share = Share.objects.get(id=share_id)
share.created = sp['submitted']
share.save()
except:
pass
def create_symlinks():
import os
# file = '/home/adam/bioshare_symlinks'
select = 'SELECT target, random_dir FROM sub_project'
results = dictfetchall(select)
base = '/data/bioshare/'
link_directory = '/data/bioshare_files/files'
os.chdir(link_directory)
for line in results:
try:
link = '00000%s' % line['random_dir']
target = base + line['target']
print '%s -> %s' % (link, target)
os.symlink(target, link)
print 'success'
except Exception, e:
print str(e)
def create_symlinks():
import os
# file = '/home/adam/bioshare_symlinks'
select = 'SELECT target, random_dir FROM sub_project'
results = dictfetchall(select)
base = '/data/bioshare/'
link_directory = '/data/bioshare_files/files'
os.chdir(link_directory)
for line in results:
try:
link = '00000%s'%line['random_dir']
target= base+line['target']
print '%s -> %s'%(link,target)
os.symlink(target,link)
print 'success'
except Exception, e:
print str(e)
def import_users():
group = Group.objects.get_or_create(name='old_accounts')[0]
print group
users = dictfetchall('select * from user')
for user in users:
try:
User.objects.get(email=user['login'])
print 'User with email %s exists' % user['login']
except:
try:
print 'Creating user %s' % user['login']
u = User(username=user['login'],email=user['login'],first_name=user['firstname'],last_name=user['lastname'])
# u.set_password(password)
u.save()
u.groups.add(group)
u.save()
except:
print 'Failed creating user %s' % user['login']
def import_users():
group = Group.objects.get_or_create(name='old_accounts')[0]
print group
users = dictfetchall('select * from user')
for user in users:
try:
User.objects.get(email=user['login'])
print 'User with email %s exists' % user['login']
except:
try:
print 'Creating user %s' % user['login']
u = User(username=user['login'],
email=user['login'],
first_name=user['firstname'],
last_name=user['lastname'])
# u.set_password(password)
u.save()
u.groups.add(group)
u.save()
except:
print 'Failed creating user %s' % user['login']
def import_permissions():
admin = User.objects.get(username='******')
select = """SELECT random_dir, login, permission FROM
(
SELECT sub_project_id, login, user.user_id, lastname, firstname, permission FROM all_user_group_permission, project, sub_project, user WHERE sub_project.project_id = project.project_id AND all_user_group_permission.group_id = project.group_id AND all_user_group_permission.user_id = user.user_id
UNION
SELECT sub_project_id, login, user.user_id, lastname, firstname, permission FROM all_user_sub_project_permission, user WHERE source LIKE 'project' AND all_user_sub_project_permission.user_id = user.user_id
UNION
SELECT sub_project_id, login, user.user_id, lastname, firstname, permission FROM all_user_sub_project_permission, user WHERE source LIKE 'sub_project' AND all_user_sub_project_permission.user_id = user.user_id
) as X join sub_project sp on X.sub_project_id = sp.sub_project_id
GROUP BY random_dir,login,permission
ORDER BY random_dir,lastname, user_id, permission"""
perms = dictfetchall(select)
perm_map = {'administer':'admin','view-project':'view_share_files','view-files':'download_share_files','upload-files':'write_to_share','delete-files':'delete_share_files'}
for p in perms:
share_id = '00000%s'%p['random_dir']
print 'treating share %s' % share_id
share = Share.objects.get(id=share_id)
user = User.objects.get(email=p['login'])
assign_perm(perm_map[p['permission']],user,share)